Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 175077.09 
• Atom Count: 10771 
• Residue Count: 1552 
• Unique protein chains: 4

1LTX

Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid

• DOI: 10.2210/pdb1LTX/pdb

• Classification: Transferase/Protein binding
• Organism(s): Rattus norvegicus
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): 3 


• Deposited: 2002-05-21 Released: 2003-05-21 
• Deposition Author(s): Pylypenko, O., Rak, A., Reents, R., Niculae, A., Thoma, N.H., Waldmann, H., Schlichting, I., Goody, R.S., Alexandrov, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.272 
• R-Value Work: 0.224 

Literature

Structure of Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase

Pylypenko, O., Rak, A., Reents, R., Niculae, A., Sidorovitch, V., Cioaca, M.D., Bessolitsyna, E., Thoma, N.H., Waldmann, H., Schlichting, I., Goody, R.S., Alexandrov, K.

(2003) Mol.Cell 11: 483-494

• PubMed: 12620235 


• PubMed Abstract: 
  

Posttranslational geranylgeranylation of Rab GTPases is catalyzed by Rab geranylgeranyltransferase (RabGGTase), which consists of a catalytic alpha/beta heterodimer and an accessory Rab escort protein (REP). The crystal structure of isoprenoid-bound RabGGTase complexed to REP-1 has been solved to 2.7 A resolution. The complex interface buries a surprisingly small surface area of ca. 680 A and is unexpectedly formed by helices 8, 10, and 12 of the RabGGTase alpha subunit and helices D and E of REP-1. We demonstrate that the affinity of RabGGTase for REP-1 is allosterically regulated by phosphoisoprenoid via a long-range trans-domain signal transduction event. Comparing the structure of REP-1 with the closely related RabGDI, we conclude that the specificity of the REP:RabGGTase interaction is defined by differently positioned phenylalanine residues conserved in the REP and GDI subfamilies.

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Related Citations: 

• Crystallization and Preliminary X-ray Diffraction Analysis of the Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase
  Rak, A.,Reents, R.,Pylypenko, O.,Niculae, A.,Sidorovitch, V.,Thoma, N.H.,Waldmann, H.,Schlichting, I.,Goody, R.S.,Alexandrov, K.
  (2001) J.STRUCT.BIOL. 136: 158




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Organizational Affiliation: 

Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT	A	567	Rattus norvegicus	Mutation(s): 0  Gene Names: Rabggta (Ggta) EC: 2.5.1.60
Find proteins for Q08602 (Rattus norvegicus) Go to UniProtKB:  Q08602

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT	B	331	Rattus norvegicus	Mutation(s): 0  Gene Names: Rabggtb (Ggtb) EC: 2.5.1.60
Find proteins for Q08603 (Rattus norvegicus) Go to UniProtKB:  Q08603

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Rab Escort Protein 1	R	650	Rattus norvegicus	Mutation(s): 3  Gene Names: Chm (Rep1)
Find proteins for P37727 (Rattus norvegicus) Go to UniProtKB:  P37727

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
AAAA	P	4	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FAR	P	FARNESYL C15 H26 JXBSHSBNOVLGHF-BUJBXKITSA-N
ZN	B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	R	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.272 
• R-Value Work: 0.224 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 68.700	α = 90.00
b = 197.300	β = 112.80
c = 85.300	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing
ProDC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-05-21 
• Released Date: 2003-05-21 
• Deposition Author(s): Pylypenko, O., Rak, A., Reents, R., Niculae, A., Thoma, N.H., Waldmann, H., Schlichting, I., Goody, R.S., Alexandrov, K.

Revision History 

• Version 1.0: 2003-05-21
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description